IEMbase 0502: PGK1-related phosphoglycerate kinase deficiency
Scope
| Field | Value |
|---|---|
| IEMbase ID | 502 |
| Nosology | 3.3.1.01 |
| Gene | PGK1 |
| External IDs | OMIM:300653; ORPHA:713 |
| Generated mapping | UNMAPPED; best scored candidate Glycogen_Storage_Disease_Type_VII.yaml (0.742) |
| Candidate DisMech targets | Glycogen_Storage_Disease_Type_VII.yaml |
| Review date | 2026-07-07 |
IEMbase phenotype signal
IEMbase represents X-linked PGK1-related phosphoglycerate kinase deficiency as muscle phosphoglycerate kinase deficiency. No treatments are listed. Biochemical rows include normal-to-increased plasma creatine kinase, decreased overall and muscle phosphoglycerate kinase activity, normal-to-increased plasma bilirubin, normal-to-increased blood reticulocytes, and normal-to-increased urine myoglobin. Clinical rows include optional hemolytic anemia, decreased RBC life span, exercise intolerance, muscle cramps, muscle pain, muscle weakness, psychomotor retardation, retinal dystrophy, and seizures.
DisMech phenotype coverage
Glycogen_Storage_Disease_Type_VII.yaml is not the correct target. The local
GSD VII file models autosomal recessive PFKM/Tarui disease with reduced
phosphofructokinase activity, exercise intolerance, hemolytic anemia, and
myoglobinuria. Those overlapping glycolysis and hemolysis signals make it a
useful neighbor, but it does not model PGK1, phosphoglycerate kinase deficiency,
X-linked inheritance, retinal dystrophy, seizures, or the PGK enzyme assay.
Concordance and completeness
Judgement: unmapped true gap; reject the GSD VII neighbor as exact coverage.
IEMbase's source disease is a multisystem X-linked glycolytic enzyme disorder with myopathic, hematologic, neurologic, and retinal features. The best-scored DisMech candidate covers a different glycolytic step and a different Mendelian entity. Shared hemolysis and exercise-intolerance vocabulary is insufficient for mapping.
Curation actions
- Keep this record unmapped until a PGK1 phosphoglycerate kinase deficiency entry is created.
- Do not substitute
Glycogen_Storage_Disease_Type_VII.yamlas exact coverage. - Preserve IEMbase prompts for X-linked inheritance, PGK activity, shortened RBC life span, hemolysis, myoglobinuria, retinal dystrophy, seizures, and psychomotor delay for a future exact entry.